This is wrong. Adding a few lines to a script would not require someone to get a writing credit for the episode. According to the WGA, for a production executive to go to arbitration to earn a writing credit:
"At the time of the credit arbitration, the production executive or production executive team must assume the burden of proving that he/she/ they had, in fact, worked on the script as a writer and had assumed full share of the writing. In the case of original screenplays, if the production executive or production executive team is the second writer he/she/ they must have contributed more than 50% of the final script to receive screenplay credit. His/her/their contribution must consist of dramatic construction; original and different scenes; characterization or character relationships; and dialogue."
Now, anyone can throw in an inside joke, and given that the credited writer is a long-time MacFarlane colleague, I assume that she can dish it out just as well as he. However, MacFarlane could have inserted the joke himself without ruining the bylines.